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aquab1t/README.md

Hi, I'm José Manuel

Oceanographer & Geospatial Scientist | PhD Marine Sciences | Former Automation Engineer

As an automation engineer turned Marine Sciences scientist, I build end-to-end data pipelines for satellite remote sensing and develop ocean hydrodynamic/lagrangian models to study ecological connectivity.

PhD Thesis results

  • ML/DL framework for Sargassum detection: spectral library of 196,037 signatures, 5 classifiers (RF, KNN, XGBoost, MLP, 1D-CNN), all macro F1 > 0.976.
  • Physics+ML Lagrangian drift model: Liu–Weisberg skill 0.533 → 0.827 (validated on 12 GPS drifters, NIOZ Weeds of Change expedition, RV Pelagia 2024).
  • GMM partition of 10-variable ocean data cube → 10 oceanographic regimes governing sargassum biogeography.

What I'm Working On

  • Kelp Forest Dynamics: Detecting Nereocystis luetkeana and Macrocystis pyrifera from Sentinel-2 imagery across the Northeast Pacific.
  • Kelp Spore Dispersal Modeling: Simulating population connectivity using the FVCOM hydrodynamic model (unstructured mesh) paired with OpenDrift/OceanParcels Lagrangian particle tracking.
  • Sargassum Detection: Classifying pelagic Sargassum in the Caribbean Sea and Equatorial Atlantic using machine learning pipelines on Aqua-MODIS, Sentinel-3 OLCI, Sentinel-2 MSI, and Landsat-8/9 OLI data. https://doi.org/10.5281/zenodo.17246345

Research Interests

  • mCDR/MRV (marine carbon dioxide removal monitoring), kelp & sargassum remote sensing, Lagrangian connectivity, and ML calibration of ocean models

Publications

  • Echevarría-Rubio, J.M., Martínez-Flores, G., Morales-Pérez, R.A. (2025). Machine and Deep Learning Framework for Sargassum Detection and Fractional Cover Estimation Using Multi-Sensor Satellite Imagery. Data, 10(11), 177. doi:10.3390/data10110177
  • Mullan, S., ... Echevarría Rubio, J.M., ... (2025). Accessible Ocean Monitoring Technologies in Developing Countries: NF-POGO Global Scholar Perspectives on Low-Cost Solutions. The Journal of Ocean Technology. doi:10.48336/ktd4-k787
  • Under review: ML velocity correction for Lagrangian Sargassum drift modelling (OpenDrift + OceanParcels cross-validation).

Tech Stack & Tools

Languages & Environments

Python R C++ Jupyter Linux

Machine Learning & Data Science

TensorFlow PyTorch Keras Scikit-Learn Pandas NumPy

Geospatial & Earth Observation

QGIS Google Earth Engine


  • Earth Observation: MODIS-Aqua, Sentinel-2 MSI, Sentinel-3 OLCI, Landsat-8/9 OLI, Ocean Color, Spectral Indices
  • Machine Learning: XGBoost, Random Forest, KNN, 1D/2D-CNN, MLP
  • Ocean Modeling: FVCOM, OpenDrift, OceanParcels, HYCOM, CMEMS, GLORYS12, ERA5, TPXO10, pyTMD
  • Geospatial Processing: GRASS, GDAL/OGR, GeoPandas, Cartopy, Rasterio, OpenDroneMap

Background

  • PhD in Marine Sciences - CICIMAR-IPN, Mexico (2022–2026). Thesis: "Dynamics of pelagic sargassum and the environmental factors controlling its proliferation in the Equatorial Atlantic and the Caribbean Sea"
  • Nippon Foundation-POGO Centre of Excellence Fellowship (2024–2025) - 10-month residential program, Memorial University + Hakai Institute + Dalhousie University
  • MSc in Marine Resources Management - CICIMAR-IPN, Mexico (2022)
  • BSc in Automation Engineering - CUJAE, Cuba (2015)

Let's Connect

LinkedIn ORCID

Pinned Loading

  1. seabed-mapping-project seabed-mapping-project Public

    Course project report and code for Geostatistics and Seabed Characterization

    Python 1 1

  2. 3d_ocean_geobody 3d_ocean_geobody Public

    This repository contains the supplementary material for the study presented at the 12th Ocean of Data Challenge. The project demonstrates a machine learning workflow to transform sparse underwater …

    HTML

  3. kelp-detection-sentinel2 kelp-detection-sentinel2 Public

    Kelp forest detection from Sentinel-2 imagery using a 2D-CNN (SepConv-SE, 4 classes, 93.7% test accuracy). Pre-trained TFLite models + 148-scene Cedros Island case study (2015–2025) analysing cloud…

    Python 1

  4. odm-dji odm-dji Public

    Interactive ODM launcher for DJI drones, auto-detects camera model and injects lens calibration

    Python

  5. sargassum-satellite-ml sargassum-satellite-ml Public

    ML pipeline for detecting pelagic Sargassum from Sentinel-2/MODIS/Landsat-8 satellite imagery. Models: XGBoost, 1D-CNN, MLP. Outputs fractional cover maps at 10m resolution. Website: https://doi.or…

    Python 1